Mapping Genetic Traits in Salmonids Using RAD Sequencing

There are many phenotypic traits that are observed to be heritable in salmonids that are of interest for conservation, supplementation, and aquaculture.  Traits such as run timing, thermal tolerance, anadromy, and disease resistance are examples.  Pedigree studies have shown strong heritability of such traits and genetic studies have identified quantitative trait loci (QTLs) and candidate loci associated with specific phenotypes.  Such studies have traditionally taken years to complete in salmonid species due to a lack of a reference genome and the types of genetic markers available.  However, it is now possible to genotype individuals at thousands of single nucleotide polymorphisms (SNPs) in a cost effective manner using next generation sequencing technology.  The RAD (Restriction site Associated DNA) sequencing approach allows for approximately 50 individual samples to be barcoded and run within the same lane of an Illumina Hi-seq instrument.  Because individual samples are barcoded, the resulting sequencing data can then be analyzed to identify and genotype greater than ten thousand SNPs per sample for a given study.  The data can also be used to create quality genetic maps if families of known pedigree fish are used.  This can provide a scaffold on which to map traits of interest to a region within a linkage group.  These dense genome scans are being used to map a variety of traits in salmonids including run timing, thermal tolerance, smoltification, and disease resistance.  Once these traits are mapped, associated markers may be used to better understand how populations adapt to local environments.  We applied this approach to examine the traits of run timing and thermal tolerance in two species of pacific salmon.